Commit a3d013bd authored by Mark van Turnhout's avatar Mark van Turnhout
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workflow updates

parent 14f7fbee
...@@ -2,4 +2,29 @@ ...@@ -2,4 +2,29 @@
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In the computer model, all the microfilaments were given certain quantitative properties with names that mean something to physicists: a `viscous damping coefficient' and an `elastic spring constant'. Never mind exactly what these mean: they are the kind of things physicists like to measure in a spring. \qauthor{Richard Dawkins \cite{Dawkins2009}} In the computer model, all the microfilaments were given certain quantitative properties with names that mean something to physicists: a `viscous damping coefficient' and an `elastic spring constant'. Never mind exactly what these mean: they are the kind of things physicists like to measure in a spring. \qauthor{Richard Dawkins \cite{Dawkins2009}}
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\chapter{Workflow} \chapter{Workflow}
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Before you can use BasilLab, you wil need to take two steps. First, add the directory that contains the (Matlab) scripts, possibly <basillab> to your Matlab search path, e.g. go (in Matlab) to that directory and issue \texttt{addpath(pwd);} on the command line.
Second, tell your local copy of BasilLab where the raw MRI-data is to be found, and where to store and for look processed MRI-data. You should use the functions \texttt{bas\_setMRIroot} and \texttt{bas\_setDataRoot} to do that (once).
The directory with the raw MRI-data (\texttt{bas\_setMRIroot}) remains untouched. The MRI-data is read and copied to the directory \texttt{<basilid>} which is created in the directory \texttt{<basilhome>} (\texttt{bas\_setDataRoot}). The link between the raw MRI-data folder inside \texttt{<MRI-root>} and \texttt{<basilid>} is \textsl{hard-coded} in \texttt{bas\_getMeta.m}.
Next the workflow can be roughly divided into four steps:
\begin{enumerate}
\item Pre-processing of (raw) MRI-data. Including reading and copying (raw) MRI-data, segmentation of MR images,and processing (segmented) MRI-data. Requires Matlab (and human intervention).
\item Building the FE model. Requires Matlab and Abaqus.
\item Running the FE model, Requires Abaqus.
\item Post-processing of FE results. Requires Abaqus.
\end{enumerate}
\section{Pre-processing of MRI-data}
\section{Building the FE model}
\section{Running the FE model}
\section{Post-processing of FE results}
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